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Construction of a foxtail millet linkage map and mapping of spikelet-tipped bristles 1(stb1) by using transposon display markers and simple sequence repeat markers with genome sequence information

Abstract

We attempted genetic analysis and mapping of a gene responsible for the trait “spikelet-tipped bristles” (stb) in foxtail millet, Setaria italica (L.) P.Beauv., as the first step in positional cloning of the gene. This trait is important not only in grain yield such as grain number per panicle of this millet but also in the evolutionary development of the “bristle grass” clade including genera Setaria, Pennisetum and Cenchrus in subfamily Panicoideae. First of all, we confirmed that this trait is controlled by a single recessive gene, using two populations of F2 plants; one was a cross combination between two Taiwanese landraces and the other was a combination between a Taiwanese landrace and a Japanese landrace. Using the latter of the two F2 populations, with transposon display (TD) markers and simple sequence repeat (SSR) markers developed previously, we constructed a genetic map with 13 linkage groups and mapped the responsible gene (stb1) on chromosome 2. We also developed novel SSR markers by using foxtail millet genome sequence information, and we finally constructed nine linkage groups corresponding to nine chromosomes with a total length of 1287.5 cM, and mapped stb1 more precisely on chromosome 2. This work suggests that the foxtail millet genome sequences recently published are useful for developing genome-wide SSR markers for constructing linkage maps and mapping genes in this millet.

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Acknowledgments

We wish to express our sincere gratitude to Dr. N. Mori and Mr. T. Hachiken, Kobe University, for their kind help in the techniques of silver staining of SSR and to Drs. N. Tomooka and M. Kawase, NIAS, for their technical assistance and advice.

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Correspondence to Kenji Fukunaga.

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Sato, K., Mukainari, Y., Naito, K. et al. Construction of a foxtail millet linkage map and mapping of spikelet-tipped bristles 1(stb1) by using transposon display markers and simple sequence repeat markers with genome sequence information. Mol Breeding 31, 675–684 (2013). https://doi.org/10.1007/s11032-012-9825-5

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Keywords

  • Genome sequences
  • Linkage map
  • Setaria italica
  • SSR (simple sequence repeat) markers
  • Spikelet-tipped bristles (stb)
  • TD (transposon display) markers